chr3-120098139-G-C

Variant names:

• chr3-120098139-G-C
• rs17811013
• ENST00000484076.1:n.267-575G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000484076.1(GSK3B-DT):​n.267-575G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0841 in 152,156 control chromosomes in the GnomAD database, including 599 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.084 (599 hom., cov: 33)
• Consequence: GSK3B-DT ENST00000484076.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 3 publications found

Genes affected

GSK3B-DT (HGNC:55635): (GSK3B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.101 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000484076.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	NR_186627.1		n.675+2361G>C		intron	N/A
	GSK3B-DT	NR_186628.1		n.676-575G>C		intron	N/A
	GSK3B-DT	NR_186629.1		n.675+2361G>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GSK3B-DT	ENST00000484076.1	TSL:1	n.267-575G>C		intron	N/A
	GSK3B-DT	ENST00000469070.2	TSL:3	n.1043-575G>C		intron	N/A
	GSK3B-DT	ENST00000485898.2	TSL:3	n.150-253G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12794 AN: 152038 Hom.: 599 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.0844

Gnomad AMR AF: 0.0832

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0412

Gnomad FIN AF: 0.0398

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0865

Gnomad OTH AF: 0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0841 AC: 12800 AN: 152156 Hom.: 599 Cov.: 33 AF XY: 0.0806 AC XY: 5994 AN XY: 74390

African (AFR) AF: 0.103 AC: 4286 AN: 41504

American (AMR) AF: 0.0831 AC: 1270 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5184

South Asian (SAS) AF: 0.0406 AC: 196 AN: 4824

European-Finnish (FIN) AF: 0.0398 AC: 421 AN: 10580

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0865 AC: 5879 AN: 67994

Other (OTH) AF: 0.101 AC: 214 AN: 2110

Alfa AF: 0.0250 Hom.: 12

Bravo AF: 0.0896

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.65
PhyloP100		-0.063

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17811013; hg19: chr3-119816986;